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(-) Description

Title :  STRUCTURE OF VCCNT-7C8C BOUND TO PYRROLO-CYTIDINE
 
Authors :  Z. L. Johnson, S. -Y. Lee
Date :  17 Apr 14  (Deposition) - 13 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane Protein, Sodium-Coupled Transporter, Pyrrolo-Cytidine, Drug Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. L. Johnson, J. H. Lee, K. Lee, M. Lee, D. Y. Kwon, J. Hong, S. Y. Lee
Structural Basis Of Nucleoside And Nucleoside Drug Selectivity By Concentrative Nucleoside Transporters.
Elife V. 3 03604 2014
PubMed-ID: 25082345  |  Reference-DOI: 10.7554/ELIFE.03604

(-) Compounds

Molecule 1 - NUPC FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: C41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VC_2352
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1DMU1Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
2NA1Ligand/IonSODIUM ION
3P0C1Ligand/Ion6-METHYL-3-(BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-2H-PYRROLO[2,3-D]PYRIMIDIN-2-ONE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1DMU3Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
2NA-1Ligand/IonSODIUM ION
3P0C3Ligand/Ion6-METHYL-3-(BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-2H-PYRROLO[2,3-D]PYRIMIDIN-2-ONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:154 , ALA A:185 , VAL A:188 , TYR A:192 , LEU A:259 , GLU A:332 , PHE A:333 , PHE A:366 , ASN A:368 , SER A:371 , ILE A:374 , HOH A:602 , HOH A:603binding site for residue P0C A 501
2AC2SOFTWAREASN A:149 , VAL A:152 , SER A:183 , ILE A:184 , HOH A:601binding site for residue NA A 502
3AC3SOFTWAREALA A:243 , ASN A:244 , ILE A:372 , ALA A:391binding site for residue DMU A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PD8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PD8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PD8)

(-) Exons   (0, 0)

(no "Exon" information available for 4PD8)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pd8 A   2 SLFMSCCGMAVLLGIAVLLSSNRKAINLRTVGGAFAIQFSLGAFILYVPWGQELLRGFSDAVSNVINYGNDGTSFLFGGLVSGKMFEVFGGGGFIFAFRVLPTLIFFSALISVLYYLGVMQWVIRILGGGLQKALGTSRAESMSAAANIFVGQTEAPLVVRPFVPKMTQSELFAVMCGGLASIAGGVLAGYASMGVKIEYLVAASFMAAPGGLLFAKLMMPETEKPQDKPANVIDAAAGGASAGLQLALNVGAMLIAFIGLIALINGMLGGIGGWFGMPELKLEMLLGWLFAPLAFLIGVPWNEATVAGEFIGLKTVANEFVAYSQFAPYLTEAAPVVLSEKTKAIISFALCGFANLSSIAILLGGLGSLAPKRRGDIARMGVKAVIAGTLSNLMAATIAGFFL 416
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    
                                                                                                                                                                                                                                                             229|                                                                                                                                                                               
                                                                                                                                                                                                                                                              241
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PD8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PD8)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (7, 7)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9KPL5_VIBCH | Q9KPL5: 3tij 4pb1 4pb2 4pd5 4pd6 4pd7 4pd9 4pda

(-) Related Entries Specified in the PDB File

3tij 3TIJ CONTAINS WILDTYPE VCCNT BOUND TO URIDINE
4pb1
4pb2
4pd5
4pd7
4pd9
4pda